Biological systems have many broken legacy "routines" that don't get called, or get called, and execute incorrectly. How do these engineers intend to deal with exception handling in this capacity?

For instance, a well known mutation known as bombay phenotype involved a precursor protein called "H protein", which then gets modified by additional cellular processes to become either A or B blood antigen. The mutation makes a defective H protein, and thus prevents the proper activation of the A or B antigen "routine".

If they try to build a programing language for cellular processes involving DNA and protein synthesis, then how will they handle exception cases, such as that one? It can be likened to the halting problem, because the question asked is "given these inputs and this program, will the program ever halt?"

Actually, most of the comments in the code for DNA are regulatory siRNA, miRNA, mRNA, and other sequences which adapt to changing environmental conditions to form different protein variants by "misfolding".

They're not garbage, they're instructions.

Naturally, some of the instructions have graffiti written on them by actual viruses. But not as much as you think.

The issue is that the "zombies", in this case, defective H proteins, stay in the cell and are NOT really dealt with. They become a new, undefined input in the system that must be accounted for when simulating other cellular processes being performed in parallel inside the cell.

This can lead to a very extensive chain ot unexpected executions and transformations. Dealing with that programmatically is going to make any computer currently in operation attempting it cry to the ghost of Alan Turing and beg for mercy.

If the goal is accurate simulation, then a (try),(catch),(finally) isn't going to work properly.

Only if there is a process for the cell to do so. Like a computer, a cell isn't magical. This is why amyloid plaque buildup in neural tissues is a fatal degenerative disease. There is no mechanism for the cells to flush the defective products they are synthesizing from the broken synthesis chain.

The real world KEEPS the defective biproduct, and simulates its impact on the rest of the system. A computer based simulation of that process that aims to be accurate, must also do so.

I'm thinking the Liver is involved in this some way. But in order for the Liver to filter this junk out, the stuff has to be placed in the blood supply. Don't "T" Cells attract White Blood cells that then drag the garbage to the Liver? Damn, feature creap, and this project hasn't even started.

Oh man! Google doesn't have anything listed for a RFC on "amyloid plaque."

Just mention in the ToC that this is a beta service and any claims of warranty or suitability for a given purpose, blah, blah, blah. Then just offer to release a patch once the exception can be reproduced and a suitable bug report has been filed.

Biological simulation engineers at Umbrella Corporation cannot guarantee the accuracy of any simulated systems created using this product, and cannot be held liable for any resulting products that may result in injury or harm to any species, including but not limited to uncontrolled anomalous tissue growths, genetically linked deformities, or the mass extinction of human kind via a zombie apochalypse.

By using this software you agree to the above enclosed terms and conditions, and to be bound to said agreeme

So... I didn't read all of the references in TFA, but this instruction set is written in LISP right? It certainly seems like the only sane language to use to develop something like this.

Then it seems like we don't have too much to worry about in regards to viruses, since few people understand LISP worth a damn.:-) I kid, but I definitely would be interested in knowing more details, since TFA was sparse on its own.

To be clear, this method of computation is not a method that is done by any natural biological system as far as I know. Their method of computation involves recombining how DNA single-strands hydrogen-bond to each other. Chemical reaction networks don't necessarily have to be done with DNA, but it's much easier to implement arbitrary networks with DNA than with other sorts of molecules since you can design how DNA sticks to other DNA. So there's really no correlation between how this code works and the "gen